Novaseq 6000

Manufactured by 10x Genomics

Sourced in Canada

The NovaSeq 6000 is a high-throughput sequencing system developed by 10x Genomics. It is designed to generate large volumes of sequencing data for a wide range of genomic applications. The NovaSeq 6000 uses advanced next-generation sequencing (NGS) technology to provide efficient and reliable sequencing performance.

Automatically generated - may contain errors

Lab products found in correlation

Spelling variants of this product

NovaSeq 6000 flow cell (2 citations) NovaSeq-6000 system (2 citations)

19 protocols using novaseq 6000

Single-Cell Immune Profiling with Multiplexed Antibodies

Check if the same lab product or an alternative is used in the 5 most similar protocols

After being processed, the 3 immune cell population fractions were stained with TotalSeq-C Human Universal Cocktail, V1.0 (BioLegend, catalog 399905), as well as Total-Seq anti–human CD72, IgG Fc, CD197 (CCR7), CD45RB, CD193 (CCR3), TCR, LAIR1 (CD395), and CD366 (Tim-3) (BioLegend, catalogs 316211, 410727, 353251, 310211, 310733, 331231, 342807, and 345049, respectively). Cells were pooled and washed using the Laminar Wash Mini system (Curiox Biosystems) before using the Chromium Next GEM Single Cell 5’ Kit v2 and Chromium Next GEM Chip K Single Cell Kit (10X Genomics).
Libraries were created using the Library Construction Kit, 5’Feature Barcode Kit, Chromium Single Cell Human BCR Amplification Kit, Dual Index Kit TT Set A (PN-1000215), and Dual Index Kit TN Set A (PN-1000250) (10X Genomics).Their quality and quantity was assessed using the Agilent Tapestation system and the Qubit Fluorometer (Invitrogen), before they were sent for sequencing on Illumina NovaSeq 6000 as per the instructions provided in 10X Genomics user guide. Sequencing was performed by SNP&SEQ Technology Platform, Science for Life Laboratory (Uppsala Biomedical Centre, Uppsala University, Sweden).

Scharf L., Axelsson H., Emmanouilidi A., Mathew N.R., Sheward D.J., Leach S., Isakson P., Smirnov I.V., Marklund E., Miron N., Andersson L.M., Gisslén M., Murrell B., Lundgren A., Bemark M, & Angeletti D. (2023). Longitudinal single-cell analysis of SARS-CoV-2–reactive B cells uncovers persistence of early-formed, antigen-specific clones. JCI Insight, 8(1), e165299.

+ Open protocol

+ Expand

Single-cell RNA-seq Library Preparation

Check if the same lab product or an alternative is used in the 5 most similar protocols

The concentration and viability of the cells were gauged using a hemocytometer and Trypan blue. After counting, single-cell libraries were prepared according to the 10× Genomics protocol CG000183 on Chromium controller (10× Genomics) and sequenced on NovaSeq6000 as paired-end 28 + 90 bp reads plus two indexing reads.
Raw sequencing data were processed using bcl2fastq2 v2.20 to convert the BCL files to fastq files while simultaneously demultiplexing. The fastq files were processed using TrimGalore v. 0.6.5 to automate quality and adapter trimming and perform quality control.

Tung V.S., Mathews F., Boruk M., Suppa G., Foronjy R., Pato M.T., Pato C.N., Knowles J.A, & Evgrafov O.V. (2023). Cultured Mesenchymal Cells from Nasal Turbinate as a Cellular Model of the Neurodevelopmental Component of Schizophrenia Etiology. International Journal of Molecular Sciences, 24(20), 15339.

+ Open protocol

+ Expand

Single-cell RNA sequencing protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

From this suspension, 16,000 cells per animal were loaded into one channel of the Chromium system using the v3 single cell reagent kit (10x Genomics, Pleasanton, CA) by the CCHMC Gene Expression Core and these libraries were sequenced as a pool on a Novaseq 6000 in the CCHMC DNA Sequencing Core. Details of scRNAseq analysis pipeline, including packages used and parameters, are found in the Supplemental Materials.

Toth A., Steinmeyer S., Kannan P., Gray J., Jackson C.M., Mukherjee S., Demmert M., Sheak J.R., Benson D., Kitzmiller J., Wayman J.A., Presicce P., Cates C., Rubin R., Chetal K., Du Y., Miao Y., Gu M., Guo M., Kalinichenko V.V., Kallapur S.G., Miraldi E.R., Xu Y., Swarr D., Lewkowich I., Salomonis N., Miller L., Sucre J.S., Whitsett J.A., Chougnet C.A., Jobe A.H., Deshmukh H, & Zacharias W.J. (2022). Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates. Science translational medicine, 14(638), eabl8574.

+ Open protocol

+ Expand

Single-cell RNA-seq of CD45+ cells

Check if the same lab product or an alternative is used in the 5 most similar protocols

To block Fc receptors, cells were incubated with 0.5 µl of TruStain FcX PLUS in 50 µl FACS of buffer. Thirty minutes later, anti-CD45 APC (1.25 µl; clone 30-F11, Biolegend; 5 µg/ml) and anti-CD19 BV421 (1.5 µl; clone 6D5, Biolegend; 1.5 µg/ml) were added in 50 µl of FACS buffer. Following incubation in darkness for 30 min at room temperature (RT), the cells were washed and resuspended in 300 µl of FACS buffer containing 0.3 µl of Sytox Green viability dye (Biolegend; 5 µM). A BD FACS Aria cell sorter was used to isolate CD45⁺ cells into RPMI + 2% FBS and resuspend them in 50 µl of PBS + 2% FBS. CD19⁺ signal was used to assess bone marrow contamination. In all samples, CD19⁺ cells represented less than 5% of total CD45⁺ cells, indicating minimal bone marrow contamination. Pooled CD45⁺ cell suspensions (n = 2–3 mice per group) were transferred to the MD Anderson Advanced Technology Genomics Core (ATGC, CA016672) for single-cell library preparation. Cell density and viability were determined using a Countess II FL auto-counter. Single cells were captured (~ 6000–9000 cells/sample) using Chromium Controller (10X Genomics), and sequencing was done by Novaseq 6000.

Nichols J.M., Pham H.V., Lee E.F., Mahalingam R, & Shepherd A.J. (2024). Single-cell analysis of age-related changes in leukocytes of diabetic mouse hindpaws. Cellular and Molecular Life Sciences: CMLS, 81(1), 146.

+ Open protocol

+ Expand

Single-cell RNA-seq library preparation

Check if the same lab product or an alternative is used in the 5 most similar protocols

For single-cell RNA-seq library preparations, cells were washed with PBS and incubated for 5 min with TrypLE, which was subsequently quenched with advanced DMEM/F12. Single cells were washed 3x with 0.4% BSA in PBS. Cells were counted using the LUNA counter and an AO/PI fluorescent stain. Cells were loaded to target 5000 following the 10xGenomics protocol for single cell 3’ prime reagent kit v3.1 (single indexes). Quality control was performed and pooled according to instructions and sequenced following the 10xGenomics guidelines at 28–8–0–91 on a NovaSeq 6000 Instrument. First a shallow sequencing run was performed to perform quality control on the libraries and estimate the number of captured cells, followed by a deeper sequencing run to reach a mean of 20 000 reads per cell. In total we captured 54 708 high quality cells after filtering, with on average 5471 cells per sample.

van der Veer B.K., Chen L., Custers C., Athanasouli P., Schroiff M., Cornelis R., Chui J.S., Finnell R.H., Lluis F, & Koh K.P. (2023). Dual functions of TET1 in germ layer lineage bifurcation distinguished by genomic context and dependence on 5-methylcytosine oxidation. Nucleic Acids Research, 51(11), 5469-5498.

+ Open protocol

+ Expand

Sequencing of Single-Cell RNA Libraries

Check if the same lab product or an alternative is used in the 5 most similar protocols

All ST libraries were sequenced according to manufacturer protocols (10X Genomics, CG000238 Rev D and CG000407 Rev A for polyA-capture and probe-based libraries, respectively). PolyA-capture ST libraries were sequenced on either the Illumina NextSeq 500/550 High Output v2.5 flowcells (Illumina, 20024907) or the Illumina NovaSeq 6000 S2 v1.5 (Illumina, 20028315). Probe-based ST libraries were sequenced at 10X Genomics on the NovaSeq 6000 according to manufacturer protocols (10X Genomics, CG000409 Rev A), with a read 2 length of 90 cycles.

Lyubetskaya A., Rabe B., Fisher A., Lewin A., Neuhaus I., Brett C., Brett T., Pereira E., Golhar R., Kebede S., Font-Tello A., Mosure K., Van Wittenberghe N., Mavrakis K.J., MacIsaac K., Chen B.J, & Drokhlyansky E. (2022). Assessment of spatial transcriptomics for oncology discovery. Cell Reports Methods, 2(11), 100340.

+ Open protocol

+ Expand

Single-Cell RNA-Seq of Motor Neurons

Check if the same lab product or an alternative is used in the 5 most similar protocols

Motor neurons were dissociated and a library preparation was conducted using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10×Genomics), and the library was sequenced on NovaSeq 6000. Details of the procedure are described in Supplementary Materials and Methods.

Imamura K., Izumi Y., Nagai M., Nishiyama K., Watanabe Y., Hanajima R., Egawa N., Ayaki T., Oki R., Fujita K., Uozumi R., Morinaga A., Hirohashi T., Fujii Y., Yamamoto T., Tatebe H., Tokuda T., Takahashi N., Morita S., Takahashi R, & Inoue H. (2022). Safety and tolerability of bosutinib in patients with amyotrophic lateral sclerosis (iDReAM study): A multicentre, open-label, dose-escalation phase 1 trial. eClinicalMedicine, 53, 101707.

+ Open protocol

+ Expand

Single-Cell Transcriptomics via 10x Genomics

Check if the same lab product or an alternative is used in the 5 most similar protocols

Sorted tetramer⁺ cells were counted on a Countless II cell counter with 0.4% trypan blue and concentrated to 300–400 cells/ml (total volume of 43.3 ml) and reverse transcribed. The libraries were generated with the 3′ kit version 3.1 chemistry (10x Genomics) and sequenced on the MiSeq system and the NovaSeq 6000.

Woodring T., Dewey C.N., Santos Dias L.D., He X., Dobson H.E., Wüthrich M, & Klein B. (2022). Distinctive populations of CD4+T cells associated with vaccine efficacy. iScience, 25(9), 104934.

+ Open protocol

+ Expand

SARS-CoV-2 Infection in Differentiated Human Airway Cells

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

scRNAseq data of ALI cultures were obtained from Ravindra et al.¹² (link) Briefly, human bronchial epithelial cells (HBECs, Lonza) were cultured at an air-liquid interface (ALI) for 28 days to achieve full mucociliary differentiation. Cultures were then challenged at the apical surface with 10⁴ plaque forming units (PFU) of SARS-CoV-2. An uninfected mock control and samples at 1dpi, 2dpi, and 3dpi were harvested with TrypLE Express Enzyme (ThermoFisher) and prepared with the Chromium Next GEM Single Cell 3’ Gel beads v3.1 kit (10X Genomics), at a target loading of 10,000 cells per sample. Libraries were generated using the Chromium Single Cell 3’ Library Kit v3.1 (10X Genomics) and sequenced on the NovaSeq 6000 using HiSeq 100 base pair reads and dual indexing, to an average depth of 31,383 reads per cell. Data were aligned and pre-processed using the 10x Genomics Cell Ranger pipeline and a combined human and SARS-CoV-2 genome. On average across samples, there were 10,000 to 15,000 counts per cell and 2,400 to 3,600 unique genes per sample. For more information, see original publication.¹² (link)

Greaney A.M., Raredon M.S., Kochugaeva M.P., Niklason L.E, & Levchenko A. (2023). SARS-CoV-2 leverages airway epithelial protective mechanism for viral infection. iScience, 26(3), 106175.

+ Open protocol

+ Expand

Single-Cell TCR Sequencing of CD138- Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols

We performed single-cell TCR sequencing on CD138- samples with available single-cell RNA sequencing data (n=9). Complementary DNA generated from barcoded CD138-immune cells using Chromium Single Cell 5’ Gene Expression and V(D)J enrichment kits by 10X Genomics was subjected to V(D)J enrichment and library preparation and sequenced on a NovaSeq 6000 instrument at the Genomics Platform of the Broad Institute of MIT & Harvard.
CellRanger v5.0.1 was used to extract FASTQ files and produce clonotype matrices⁵⁰. When multiple alignments were called for a single chain, the alignment with the most UMIs was selected, and when multiple chains were called for a single cell barcode, the top two chains in terms of UMI counts were selected.

Nadeem O., Aranha M.P., Redd R., Timonian M., Magidson S., Lightbody E.D., Alberge J.B., Bertamini L., Dutta A.K., El-Khoury H., Bustoros M., Laubach J.P., Bianchi G., O’Donnell E., Wu T., Tsuji J., Anderson K., Getz G., Trippa L., Richardson P.G., Sklavenitis-Pistofidis R, & Ghobrial I.M. (2024). Long-Term Follow-Up Defines the Population That Benefits from Early Interception in a High-Risk Smoldering Multiple Myeloma Clinical Trial Using the Combination of Ixazomib, Lenalidomide, and Dexamethasone. medRxiv.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!